The Headunit's ground and memory power, usually a yellow wire, need to be run to one of the power and ground lugs on one of the amps. Also make sure the gains are set correctly, if too high, it will amplify any noise.

Phil White helped a bunch of us out with this same problem. As TM said you need to get your amps and stereo on the same battery's. Your HU is likely wired to your starting battery. I re did mine and it's perfect no alt whine at all. I'll see if I can find the diagram for you but essentially wire the ground and power to your biggest amps ground and power but you also have to rewire the remote turn on too. I tried to get away without doing the last part and it didn't work. You either have to wire it off your key via a relay or if you use a toggle switch just straight to that.

Hate and TigeMike are right; you need to isolate the stereo/head unit wiring as shown in the diagram above and double check your gains...

I really need to redraw a new version of that drawing. As Hate shared, the relay shown in the bottom middle is unnecessary unless you are using more than two amps.

Also, the relay to the left is only shown for those boats that have a key switch that can turn to an "accessory-only" position. If you are one of the lucky souls who has a rocker switch on the dash to turn the stereo on and off, you can just connect both the yellow and the red head unit power wires straight to the amp's 12v+ power connection, with the red wire going through the dash stereo switch.

The stereo in my boat is totally aftermarket, there was never a stereo in the boat when I bought it (86 ski nautique 2001) so I believe I just spliced it in to the power and grounded it to something else. So you're correct when you say its set up to run off my starting battery.

Why can't I just wire the HU straight to my stereo batteries instead of the amp? The stereo batteries are actually closer to the HU than the amp

I don't think that it has anything to do with your noise, but most gurus do not recommend running both lead acid batteries and AGM batteries. They charge at different rates and are likely to cause one or the other to fail prematurely.

Talltigeguy- I agree with you. Although I have my stuff 2 diff style batteries all hooked up to a perko switch I never have my switch set to all. I only run my switch on 1. I charge my batteries when I am done on the lake with trickle chargers. My starting batt and stereo batteries are on different chargers.

I just swaped locations of my amps with each other. I made no wiring changes. When I started it up it had a wine that was not there before. I disconected the rca's and plugged them back in.No difference. I then twisted the rca's in the jack as they were plugged in and the wine stopped. May want to check out you rca's while its running. It's quick and easy.